chr16-28053506-T-C

Position:

• chr16-28053506-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001109763.2(GSG1L):​c.349+9570A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,082 control chromosomes in the GnomAD database, including 46,609 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.77 (46609 hom., cov: 31)
• Consequence: GSG1L NM_001109763.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

Genes affected

GSG1L (HGNC:28283): (GSG1 like) Predicted to be involved in regulation of AMPA receptor activity. Predicted to be located in postsynaptic density. Predicted to be active in Schaffer collateral - CA1 synapse; glutamatergic synapse; and plasma membrane. Predicted to be integral component of postsynaptic density membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GSG1L	NM_001109763.2	c.349+9570A>G		intron_variant		ENST00000447459.7	NP_001103233.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSG1L	ENST00000447459.7	c.349+9570A>G		intron_variant		2	NM_001109763.2	ENSP00000394954.2
GSG1L	ENST00000395724.7	c.349+9570A>G		intron_variant		1		ENSP00000379074.3
GSG1L	ENST00000562611.1	n.112+9570A>G		intron_variant		3		ENSP00000454942.1

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117433 AN: 151964 Hom.: 46572 Cov.: 31

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.800

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.773 AC: 117526 AN: 152082 Hom.: 46609 Cov.: 31 AF XY: 0.777 AC XY: 57748 AN XY: 74346

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.878

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.896

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.802

Alfa AF: 0.779 Hom.: 3507

Bravo AF: 0.766

Asia WGS AF: 0.870 AC: 3025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs205412; hg19: chr16-28064827;